MRC WIMM Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.
PLoS Comput Biol. 2020 Sep 8;16(9):e1008195. doi: 10.1371/journal.pcbi.1008195. eCollection 2020 Sep.
We present VALERIE (Visualising alternative splicing events from single-cell ribonucleic acid-sequencing experiments), an R package for visualising alternative splicing events at single-cell resolution. To explore any given specified genomic region, corresponding to an alternative splicing event, VALERIE generates an ensemble of informative plots to visualise cell-to-cell heterogeneity of alternative splicing profiles across single cells and performs statistical tests to compare percent spliced-in (PSI) values across the user-defined groups of cells. Among the features available, VALERIE displays PSI values, in lieu of read coverage, which is more suitable for representing alternative splicing profiles for a large number of samples typically generated by single-cell RNA-sequencing experiments. VALERIE is available on the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/VALERIE/index.html.
我们提出了 VALERIE（从单细胞 RNA 测序实验中可视化可变剪接事件），这是一个用于以单细胞分辨率可视化可变剪接事件的 R 包。为了探索任何给定的指定基因组区域，对应于一个可变剪接事件，VALERIE 生成了一组信息丰富的图，以可视化单细胞中可变剪接谱的细胞间异质性，并对用户定义的细胞组进行 PSI 值进行统计检验。在可用的功能中，VALERIE 显示 PSI 值，而不是读取覆盖率，这更适合表示通常由单细胞 RNA-seq 实验生成的大量样本的可变剪接谱。VALERIE 可在 Comprehensive R Archive Network（CRAN）上获得：https://cran.r-project.org/web/packages/VALERIE/index.html。
